Cleanup, mostly formatting

.gitignore

@@ -6,8 +6,6 @@ michael-local
 GPATH
 GTAGS
 GRTAGS
-.idea
-*.iml
 # OS generated files #
 ######################
 .DS_Store
@@ -32,7 +30,7 @@ scripts/installer/dvinstall/
 oauth-credentials.md
 
 /src/main/webapp/oauth2/newAccount.html
-#scripts/api/setup-all.sh*
+scripts/api/setup-all.sh*
 
 # ctags generated tag file
 tags

doc/sphinx-guides/source/installation/config.rst

@@ -179,12 +179,12 @@ To configure Shibboleth see the :doc:`shibboleth` section and to configure OAuth
 
 The ``authenticationproviderrow`` database table controls which "authentication providers" are available within Dataverse. Out of the box, a single row with an id of "builtin" will be present. For each user in Dataverse, the ``authenticateduserlookup`` table will have a value under ``authenticationproviderid`` that matches this id. For example, the default "dataverseAdmin" user will have the value "builtin" under  ``authenticationproviderid``. Why is this important? Users are tied to a specific authentication provider but conversion mechanisms are available to switch a user from one authentication provider to the other. As explained in the :doc:`/user/account` section of the User Guide, a graphical workflow is provided for end users to convert from the "builtin" authentication provider to a remote provider. Conversion from a remote authentication provider to the builtin provider can be performed by a sysadmin with access to the "admin" API. See the :doc:`/api/native-api` section of the API Guide for how to list users and authentication providers as JSON.
 
-Enabling a second authentication provider will result in the Log In page showing additional providers for your users to choose from. By default, the Log In page will show the "builtin" provider, but you can adjust this via the ``:DefaultAuthProvider`` configuration option.
+Enabling a second authentication provider will result in the Log In page showing additional providers for your users to choose from. By default, the Log In page will show the "builtin" provider, but you can adjust this via the ``:DefaultAuthProvider`` configuration option. 
 
 "Remote only" mode should be considered experimental until https://github.com/IQSS/dataverse/issues/2974 is resolved. For now, "remote only" means:
 
 - Shibboleth or OAuth has been enabled.
-- ``:AllowSignUp`` is set to "false" per the :doc:`config` section to prevent users from creating local accounts via the web interface. Please note that local accounts can also be created via API, and the way to prevent this is to block the ``builtin-users`` endpoint or scramble (or remove) the ``BuiltinUsers.KEY`` database setting per the :doc:`config` section.
+- ``:AllowSignUp`` is set to "false" per the :doc:`config` section to prevent users from creating local accounts via the web interface. Please note that local accounts can also be created via API, and the way to prevent this is to block the ``builtin-users`` endpoint or scramble (or remove) the ``BuiltinUsers.KEY`` database setting per the :doc:`config` section. 
 - The "builtin" authentication provider has been disabled. Note that disabling the builting auth provider means that the API endpoint for converting an account from a remote auth provider will not work. This is the main reason why https://github.com/IQSS/dataverse/issues/2974 is still open. Converting directly from one remote authentication provider to another (i.e. from GitHub to Google) is not supported. Conversion from remote is always to builtin. Then the user initiates a conversion from builtin to remote. Note that longer term, the plan is to permit multiple login options to the same Dataverse account per https://github.com/IQSS/dataverse/issues/3487 (so all this talk of conversion will be moot) but for now users can only use a single login option, as explained in the :doc:`/user/account` section of the User Guide. In short, "remote only" might work for you if you only plan to use a single remote authentication provider such that no conversion between remote authentication providers will be necessary.
 
 File Storage: Local Filesystem vs. Swift vs. S3
@@ -1268,7 +1268,6 @@ This sets the base name (without dot and extension), if not set it defaults to '
 ``curl -X PUT -d domainstats http://localhost:8080/api/admin/settings/:PiwikAnalyticsTrackerFileName``
 
 
-
 :FileFixityChecksumAlgorithm
 ++++++++++++++++++++++++++++
 

downloads/.gitignore

@@ -2,4 +2,3 @@ glassfish-4.1.zip
 solr-7.3.0.tgz
 weld-osgi-bundle-2.2.10.Final-glassfish4.jar
 schemaSpy_5.0.0.jar
-solr-4.6.0.tgz

src/main/java/edu/harvard/iq/dataverse/CustomizationFilesServlet.java

@@ -19,7 +19,6 @@
 import javax.servlet.http.HttpServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
-
 import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
 import javax.ejb.EJB;
 import org.apache.commons.io.IOUtils;
@@ -30,11 +29,11 @@
  */
 @WebServlet(name = "CustomizationFilesServlet", urlPatterns = {"/CustomizationFilesServlet"})
 public class CustomizationFilesServlet extends HttpServlet {
-
+    
     @EJB
     SettingsServiceBean settingsService;
-
-
+            
+            
     /**
      * Processes requests for both HTTP <code>GET</code> and <code>POST</code>
      * methods.
@@ -45,8 +44,8 @@ public class CustomizationFilesServlet extends HttpServlet {
      * @throws IOException if an I/O error occurs
      */
     protected void processRequest(HttpServletRequest request, HttpServletResponse response)
-        throws ServletException, IOException {
-        response.setContentType("text/html;charset=UTF-8");
+            throws ServletException, IOException {
+        response.setContentType("text/html;charset=UTF-8");               
 
         String customFileType = request.getParameter("customFileType");
         String filePath = getFilePath(customFileType);
@@ -64,7 +63,7 @@ protected void processRequest(HttpServletRequest request, HttpServletResponse re
 
                 StringBuilder responseData = new StringBuilder();
                 try (PrintWriter out = response.getWriter()) {
-
+                    
                     while ((line = in.readLine()) != null) {
                         responseData.append(line);
                         out.println(line);
@@ -90,37 +89,37 @@ protected void processRequest(HttpServletRequest request, HttpServletResponse re
         }
 
     }
-
+    
     private String getFilePath(String fileTypeParam){
 
         String nonNullDefaultIfKeyNotFound = "";
-
+        
         if (fileTypeParam.equals(CustomizationConstants.fileTypeHomePage)) {
-
+            
             // Homepage
             return settingsService.getValueForKey(SettingsServiceBean.Key.HomePageCustomizationFile, nonNullDefaultIfKeyNotFound);
-
+                
         } else if (fileTypeParam.equals(CustomizationConstants.fileTypeHeader)) {
-
+            
             // Header
             return settingsService.getValueForKey(SettingsServiceBean.Key.HeaderCustomizationFile, nonNullDefaultIfKeyNotFound);
 
         } else if (fileTypeParam.equals(CustomizationConstants.fileTypeFooter)) {
-
+            
             // Footer        
             return settingsService.getValueForKey(SettingsServiceBean.Key.FooterCustomizationFile, nonNullDefaultIfKeyNotFound);
-
+        
         } else if (fileTypeParam.equals(CustomizationConstants.fileTypeStyle)) {
-
+            
             // Style (css)               
             return settingsService.getValueForKey(SettingsServiceBean.Key.StyleCustomizationFile, nonNullDefaultIfKeyNotFound);
-
+        
         } else if (fileTypeParam.equals(CustomizationConstants.fileTypeLogo)) {
 
             // Logo for installation - appears in header               
             return settingsService.getValueForKey(SettingsServiceBean.Key.LogoCustomizationFile, nonNullDefaultIfKeyNotFound);
         }
-
+        
 
         return "";
     }
@@ -136,7 +135,7 @@ private String getFilePath(String fileTypeParam){
      */
     @Override
     protected void doGet(HttpServletRequest request, HttpServletResponse response)
-        throws ServletException, IOException {
+            throws ServletException, IOException {
         processRequest(request, response);
     }
 
@@ -150,7 +149,7 @@ protected void doGet(HttpServletRequest request, HttpServletResponse response)
      */
     @Override
     protected void doPost(HttpServletRequest request, HttpServletResponse response)
-        throws ServletException, IOException {
+            throws ServletException, IOException {
         processRequest(request, response);
     }
 

src/main/java/edu/harvard/iq/dataverse/DatasetPage.java

@@ -207,7 +207,7 @@ public enum DisplayMode {
     @Inject
     ThumbnailServiceWrapper thumbnailServiceWrapper;
     @Inject
-    SettingsWrapper settingsWrapper;
+    SettingsWrapper settingsWrapper; 
     @Inject 
     ProvPopupFragmentBean provPopupFragmentBean;
 
@@ -1202,7 +1202,7 @@ private void updateDatasetFieldInputLevels() {
             Format:  {  DatasetFieldType.id : DatasetField }
          --------------------------------------------------------- */
         // Initialize Map
-        Map<Long, DatasetField> mapDatasetFields = new HashMap<>();
+        Map<Long, DatasetField> mapDatasetFields = new HashMap<>();   
 
         // Populate Map
          for (DatasetField dsf : workingVersion.getFlatDatasetFields()) {
@@ -1560,8 +1560,7 @@ private String init(boolean initFull) {
         try {
             privateUrl = commandEngine.submit(new GetPrivateUrlCommand(dvRequestService.getDataverseRequest(), dataset));
             if (privateUrl != null) {
-                JH.addMessage(FacesMessage.SEVERITY_INFO, BundleUtil.getStringFromBundle("dataset.privateurl.infoMessageAuthor", Arrays
-                    .asList(getPrivateUrlLink(privateUrl))));
+                JH.addMessage(FacesMessage.SEVERITY_INFO, BundleUtil.getStringFromBundle("dataset.privateurl.infoMessageAuthor", Arrays.asList(getPrivateUrlLink(privateUrl))));
             }
         } catch (CommandException ex) {
             // No big deal. The user simply doesn't have access to create or delete a Private URL.
@@ -1781,7 +1780,7 @@ private void resetVersionUI() {
                                 if (subField.getDatasetFieldType().getName().equals(DatasetFieldConstant.authorIdValue)) {
                                     subField.getDatasetFieldValues().get(0).setValue(creatorOrcidId);
                                 }
-                                if (subField.getDatasetFieldType().getName().equals(DatasetFieldConstant.authorIdType)) {
+                                if (subField.getDatasetFieldType().getName().equals(DatasetFieldConstant.authorIdType)) {  
                                    DatasetFieldType authorIdTypeDatasetField = fieldService.findByName(DatasetFieldConstant.authorIdType);
                                    subField.setSingleControlledVocabularyValue(fieldService.findControlledVocabularyValueByDatasetFieldTypeAndStrValue(authorIdTypeDatasetField, "ORCID", true));
                                 }                                
@@ -2071,7 +2070,7 @@ private String releaseDataset(boolean minor) {
                     new PublishDatasetCommand(dataset, dvRequestService.getDataverseRequest(), minor)
                 );
                 dataset = result.getDataset();
-                // Sucessfully executing PublishDatasetCommand does not guarantee that the dataset
+                // Sucessfully executing PublishDatasetCommand does not guarantee that the dataset 
                 // has been published. If a publishing workflow is configured, this may have sent the 
                 // dataset into a workflow limbo, potentially waiting for a third party system to complete 
                 // the process. So it may be premature to show the "success" message at this point. 
@@ -2714,7 +2713,7 @@ public String save() {
             if (editMode == EditMode.CREATE) {                
                 if ( selectedTemplate != null ) {
                     if ( isSessionUserAuthenticated() ) {
-                        cmd = new CreateNewDatasetCommand(dataset, dvRequestService.getDataverseRequest(), false, selectedTemplate);
+                        cmd = new CreateNewDatasetCommand(dataset, dvRequestService.getDataverseRequest(), false, selectedTemplate); 
                     } else {
                         JH.addMessage(FacesMessage.SEVERITY_FATAL, BundleUtil.getStringFromBundle("dataset.create.authenticatedUsersOnly"));
                         return null;
@@ -2965,7 +2964,7 @@ public boolean isLockedInProgress() {
 
     public boolean isDatasetLockedInWorkflow() {
         return (dataset != null) 
-                ? dataset.isLockedFor(DatasetLock.Reason.Workflow)
+                ? dataset.isLockedFor(DatasetLock.Reason.Workflow) 
                 : false;
     }
 
@@ -3464,7 +3463,7 @@ public boolean isDesignatedDatasetThumbnail (FileMetadata fileMetadata) {
      * Items for the "Designated this image as the Dataset thumbnail: 
      */
 
-    private FileMetadata fileMetadataSelectedForThumbnailPopup = null;
+    private FileMetadata fileMetadataSelectedForThumbnailPopup = null; 
 
     public void  setFileMetadataSelectedForThumbnailPopup(FileMetadata fm){
        fileMetadataSelectedForThumbnailPopup = fm; 
@@ -3538,7 +3537,7 @@ public void saveAsDesignatedThumbnail() {
      * Items for the "Tags (Categories)" popup.
      *
      */
-    private FileMetadata fileMetadataSelectedForTagsPopup = null;
+    private FileMetadata fileMetadataSelectedForTagsPopup = null; 
 
     public void  setFileMetadataSelectedForTagsPopup(){
 
@@ -3849,7 +3848,7 @@ private void removeUnusedFileTagsFromDataset() {
      * Items for the "Advanced (Ingest) Options" popup. 
      * 
      */
-    private FileMetadata fileMetadataSelectedForIngestOptionsPopup = null;
+    private FileMetadata fileMetadataSelectedForIngestOptionsPopup = null; 
 
     public void  setFileMetadataSelectedForIngestOptionsPopup(FileMetadata fm){
        fileMetadataSelectedForIngestOptionsPopup = fm; 

src/main/java/edu/harvard/iq/dataverse/LoginPage.java

@@ -119,7 +119,7 @@ public void init() {
         authProvider = authSvc.getAuthenticationProvider(systemConfig.getDefaultAuthProvider());
         random = new Random();
     }
-    
+
     public List<AuthenticationProviderDisplayInfo> listCredentialsAuthenticationProviders() {
         List<AuthenticationProviderDisplayInfo> infos = new LinkedList<>();
         for ( String id : authSvc.getAuthenticationProviderIdsOfType( CredentialsAuthenticationProvider.class ) ) {

src/main/java/edu/harvard/iq/dataverse/api/BatchServiceBean.java

@@ -27,7 +27,7 @@
  */
 @Stateless
 public class BatchServiceBean {
-    private static final Logger logger = Logger.getLogger(BatchServiceBean.class.getCanonicalName());
+ private static final Logger logger = Logger.getLogger(BatchServiceBean.class.getCanonicalName());
 
     @EJB
     DataverseServiceBean dataverseService;
@@ -41,43 +41,40 @@ public void processFilePath(String fileDir, String parentIdtf, DataverseRequest
         PrintWriter validationLog = null;
         PrintWriter cleanupLog = null;
         try {
-            JsonArrayBuilder status = Json.createArrayBuilder();
-            Date timestamp = new Date();
-
-            SimpleDateFormat formatter = new SimpleDateFormat("yyyy-MM-dd_HH:mm:ss");
+        JsonArrayBuilder status = Json.createArrayBuilder();
+        Date timestamp = new Date();
 
-            validationLog = new PrintWriter(new FileWriter( "../logs/validationLog"+  formatter.format(timestamp)+".txt"));
-            cleanupLog = new PrintWriter(new FileWriter( "../logs/cleanupLog"+  formatter.format(timestamp)+".txt"));
-            File dir = new File(fileDir);
-            if (dir.isDirectory()) {
-                for (File file : dir.listFiles()) {
-                    if (null != file) {
-                        if (!file.isHidden()) {
-                            if (file.isDirectory()) {
-                                try {
-                                    status.add(handleDirectory(dataverseRequest, file, importType, validationLog,
-                                        cleanupLog, createDV));
-                                } catch (ImportException e) {
-                                    logger.log(Level.SEVERE, "Exception in handleDirectory() for " + file.getName(), e);
-                                }
-                            } else {
-                                try {
-                                    status.add(importService.handleFile(dataverseRequest, owner, file, importType,
-                                        validationLog, cleanupLog));
-                                } catch (ImportException e) {
-                                    logger.log(Level.SEVERE, "Exception in handleFile() for " + file.getName(), e);
-                                }
+        SimpleDateFormat formatter = new SimpleDateFormat("yyyy-MM-dd_HH:mm:ss");
 
-                            }
+        validationLog = new PrintWriter(new FileWriter( "../logs/validationLog"+  formatter.format(timestamp)+".txt"));
+        cleanupLog = new PrintWriter(new FileWriter( "../logs/cleanupLog"+  formatter.format(timestamp)+".txt"));
+        File dir = new File(fileDir);
+        if (dir.isDirectory()) {
+            for (File file : dir.listFiles()) {
+                if (!file.isHidden()) {
+                    if (file.isDirectory()) {
+                        try {
+                            status.add(handleDirectory(dataverseRequest, file, importType, validationLog, cleanupLog, createDV));
+                        } catch (ImportException e) {
+                            logger.log(Level.SEVERE, "Exception in handleDirectory() for "+ file.getName(),e);
                         }
+                    } else {
+                        try {
+                            status.add(importService.handleFile(dataverseRequest, owner, file, importType, validationLog, cleanupLog));
+                        } catch(ImportException e) {
+                             logger.log(Level.SEVERE, "Exception in handleFile() for "+ file.getName(),e);
+                        }
+
                     }
                 }
-            } else {
-                status.add(importService.handleFile(dataverseRequest, owner, dir, importType, validationLog, cleanupLog));
-
             }
-        } catch (Exception e) {
-            logger.log(Level.SEVERE, "Exception in processFilePath()", e);
+        } else {
+            status.add(importService.handleFile(dataverseRequest, owner, dir, importType, validationLog, cleanupLog));
+
+        }
+        }
+        catch(Exception e) {
+                logger.log(Level.SEVERE, "Exception in processFilePath()", e);
         } finally {
             validationLog.close();
             cleanupLog.close();
@@ -98,20 +95,16 @@ public JsonArrayBuilder handleDirectory(DataverseRequest dataverseRequest, File
             }
         }
         for (File file : dir.listFiles()) {
-            if (null != file) {
-                if (!file.isHidden()) {
-                    try {
-                        JsonObjectBuilder fileStatus = importService.handleFile(dataverseRequest, owner, file,
-                            importType, validationLog, cleanupLog);
-                        status.add(fileStatus);
-                    } catch (ImportException | IOException e) {
-                        status.add(Json.createObjectBuilder().add("importStatus",
-                            "Exception importing " + file.getName() + ", message = " + e.getMessage()));
-                    }
+            if (!file.isHidden()) {
+                try {
+                    JsonObjectBuilder fileStatus = importService.handleFile(dataverseRequest, owner, file, importType, validationLog, cleanupLog);
+                    status.add(fileStatus);
+                } catch (ImportException | IOException e) {
+                    status.add(Json.createObjectBuilder().add("importStatus", "Exception importing " + file.getName() + ", message = " + e.getMessage()));
                 }
             }
         }
         return status;
     }
 
-}
+}